SMTL ID : 1g6i.1

Crystal structure of the yeast alpha-1,2-mannosidase with bound 1-deoxymannojirimycin at 1.59 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

1 x NAG- NDG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NDG-BMA-MAN-MAN-MAN-MAN.1: 4 residues within 4Å: Chain A: L.94, N.97, L.152, E.511 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.94 Hydrogen bonds: A:N.97

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN.2: 8 residues within 4Å: Chain A: D.169, A.172, L.173, L.176, N.225, T.227, Y.228, L.231 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.176, A:L.231

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 4 residues within 4Å: Chain A: N.118, N.156, T.158, V.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.118, A:N.156 Water bridges: A:N.118

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: T.521 Ligands: DMJ.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.521, A:T.521, H2O.5, H2O.8

1 x DMJ: 1-DEOXYMANNOJIRIMYCIN(Non-covalent)

DMJ.5: 11 residues within 4Å: Chain A: I.136, R.137, L.339, R.429, P.430, E.431, F.495, E.499, T.521, E.522 Ligands: CA.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.429, A:E.431, A:E.499, A:T.521, A:E.522 Water bridges: A:R.137, A:T.521

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Herscovics, A. et al., Structure and function of Class I a1,2-mannosidases involved in glycoprotein biosynthesis. CARBOHYDRATE BIOENGINEERING. INTERDISCIPLINARY APPROACHES. (2002)

Release Date

2003-06-24

Peptides

CLASS I ALPHA-1,2-MANNOSIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CLASS I ALPHA-1,2-MANNOSIDASE